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- PDB-6l4u: Structure of the PSI-FCPI supercomplex from diatom -

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Basic information

Entry
Database: PDB / ID: 6l4u
TitleStructure of the PSI-FCPI supercomplex from diatom
Components
  • (Fucoxanthin chlorophyll a/c-binding protein ...) x 16
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
  • Unknown protein 1
KeywordsELECTRON TRANSPORT / Photosystem I
Function / homology
Function and homology information


Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER
Similarity search - Component
Biological speciesChaetoceros gracilis (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNagao, R. / Kato, K. / Miyazaki, N. / Akita, F. / Shen, J.R.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex.
Authors: Ryo Nagao / Koji Kato / Kentaro Ifuku / Takehiro Suzuki / Minoru Kumazawa / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c- ...Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.
History
DepositionOct 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
1u: Unknown protein 1
2u: Photosystem I reaction center subunit Psa28
1: Fucoxanthin chlorophyll a/c-binding protein Lhcr15
2: Fucoxanthin chlorophyll a/c-binding protein Lhcr8
3: Fucoxanthin chlorophyll a/c-binding protein Lhcr2
4: Fucoxanthin chlorophyll a/c-binding protein Lhcr9
5: Fucoxanthin chlorophyll a/c-binding protein Lhcr11
6: Fucoxanthin chlorophyll a/c-binding protein Lhcr12
7: Fucoxanthin chlorophyll a/c-binding protein Lhcr10
8: Fucoxanthin chlorophyll a/c-binding protein Lhcr4
9: Fucoxanthin chlorophyll a/c-binding protein Lhcf6
10: Fucoxanthin chlorophyll a/c-binding protein Lhcr3
11: Fucoxanthin chlorophyll a/c-binding protein Lhcq13
12: Fucoxanthin chlorophyll a/c-binding protein Lhcq3
13: Fucoxanthin chlorophyll a/c-binding protein Lhcq11
14: Fucoxanthin chlorophyll a/c-binding protein Lhcq10
15: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
16: Fucoxanthin chlorophyll a/c-binding protein Lhcq5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)997,683455
Polymers673,97828
Non-polymers323,705427
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 /


Mass: 83648.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 /


Mass: 81897.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Protein , 2 types, 2 molecules C1u

#3: Protein Photosystem I iron-sulfur center /


Mass: 8807.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#11: Protein Unknown protein 1


Mass: 11081.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJLM2u

#4: Protein Photosystem I reaction center subunit II /


Mass: 15594.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#5: Protein Photosystem I reaction center subunit IV /


Mass: 7621.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#6: Protein Photosystem I reaction center subunit III /


Mass: 20445.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 3944.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4882.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#9: Protein Photosystem I reaction center subunit XI /


Mass: 16148.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#10: Protein/peptide Photosystem I reaction center subunit XII /


Mass: 3241.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#12: Protein Photosystem I reaction center subunit Psa28 /


Mass: 12899.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Fucoxanthin chlorophyll a/c-binding protein ... , 16 types, 16 molecules 12345678910111213141516

#13: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr15


Mass: 24881.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#14: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr8


Mass: 21727.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#15: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr2


Mass: 21558.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#16: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr9


Mass: 22933.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#17: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr11


Mass: 29512.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#18: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr12


Mass: 22362.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#19: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr10


Mass: 32238.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#20: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr4


Mass: 29704.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#21: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcf6


Mass: 23517.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#22: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcr3


Mass: 22216.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#23: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq13


Mass: 24842.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#24: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq3


Mass: 21318.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#25: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq11


Mass: 25994.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#26: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq10


Mass: 26875.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#27: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq8


Mass: 30545.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#28: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq5


Mass: 23533.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Sugars , 1 types, 21 molecules

#35: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 562 molecules

#29: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#30: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 221 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#31: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#32: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#33: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#34: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#36: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C45H86O10
#37: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate / Fucoxanthin / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C42H58O6
#38: Chemical...
ChemComp-KC1 / Chlorophyll c1 / Chlorophyll c


Mass: 610.941 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#39: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H54O3
#40: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-FCPI / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Molecular weightValue: 0.64 MDa / Experimental value: NO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMES-NaOHMES-NaOH1
20.02 %DDMDDM1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4CTFFIND4CTF correction
7UCSF Chimera1.12model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2689965
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 470801 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient

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